scholarly journals Multi-reference spectral library yields almost complete coverage of heterogeneous LC-MS/MS data sets

2017 ◽  
Author(s):  
Constantin Ammar ◽  
Evi Berchtold ◽  
Gergely Csaba ◽  
Andreas Schmidt ◽  
Axel Imhof ◽  
...  
Keyword(s):  
Systematic Evaluation ◽  
Spectral Library ◽  
Spectral Variability ◽  
Complete Coverage ◽  
Multiple Characteristic ◽  
Experimental Conditions ◽  
Data Set ◽  
Custom Made ◽  
Public Repositories ◽  
Peptide Charge

AbstractSpectral libraries play a central role in the analysis of data-independent-acquisition (DIA) proteomics experiments. A main assumption in current spectral library tools is that a single characteristic intensity pattern (CIP) suffices to describe the fragmentation of a peptide in a particular charge state (peptide charge pair). However, we find that this is often not the case. We carry out a systematic evaluation of spectral variability over public repositories and in-house datasets. We show that spectral variability is widespread and partly occurs under fixed experimental conditions. Using clustering of preprocessed spectra, we derive a limited number of Multiple Characteristic Intensity Patterns (MCIPs) for each peptide charge pair, which allow almost complete coverage of our heterogeneous dataset without affecting the false discovery rate. We show that a MCIP library derived from public repositories performs in most cases similar to a “custom-made” spectral library, which has been acquired under identical experimental conditions as the query spectra. We apply the MCIP approach to a DIA data set and observe a significant increase in peptide recognition. We propose the MCIP approach as an easy-to-implement addition to current spectral library search engines and as a new way to utilize the data stored in spectral repositories.

scholarly journals N-Linked Glycopeptide Identification Based on Open Mass Spectral Library Search

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Zhiwu An ◽  
Qingbo Shu ◽  
Hao Lv ◽  
Lian Shu ◽  
Jifeng Wang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Human Cancer ◽  
Cancer Cell Line ◽  
Peptide Identification ◽  
High Energy ◽  
Mass Spectral Library ◽  
Spectral Library ◽  
Data Set ◽  
Library Search ◽  
Mass Spectral

Confident characterization of intact glycopeptides is a challenging task in mass spectrometry-based glycoproteomics due to microheterogeneity of glycosylation, complexity of glycans, and insufficient fragmentation of peptide bones. Open mass spectral library search is a promising computational approach to peptide identification, but its potential in the identification of glycopeptides has not been fully explored. Here we present pMatchGlyco, a new spectral library search tool for intact N-linked glycopeptide identification using high-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS) data. In pMatchGlyco, (1) MS/MS spectra of deglycopeptides are used to create spectral library, (2) MS/MS spectra of glycopeptides are matched to the spectra in library in an open (precursor tolerant) manner and the glycans are inferred, and (3) a false discovery rate is estimated for top-scored matches above a threshold. The efficiency and reliability of pMatchGlyco were demonstrated on a data set of mixture sample of six standard glycoproteins and a complex glycoprotein data set generated from human cancer cell line OVCAR3.

scholarly journals The Hubble PanCET program: Transit and Eclipse Spectroscopy of the Hot-Jupiter WASP-74b

2021 ◽  
Vol 162 (6) ◽  
pp. 271
Author(s):  
Guangwei Fu ◽  
Drake Deming ◽  
Erin May ◽  
Kevin Stevenson ◽  
David K. Sing ◽  
...  
Keyword(s):  
Rayleigh Scattering ◽  
Hubble Space Telescope ◽  
Absorption Feature ◽  
Spectral Library ◽  
Data Set ◽  
Space Telescope ◽  
Methane Absorption ◽  
James Webb Space Telescope ◽  
Hot Jupiter

Abstract Planets are like children with each one being unique and special. A better understanding of their collective properties requires a deeper understanding of each planet. Here we add the transit and eclipse spectra of hot-Jupiter WASP-74b into the ever growing data set of exoplanet atmosphere spectral library. With six transits and three eclipses using the Hubble Space Telescope and Spitzer Space Telescope (Spitzer), we present the most complete and precise atmospheric spectra of WASP-74b. We found no evidence for TiO/VO nor super-Rayleigh scattering reported in previous studies. The transit shows a muted water feature with strong Rayleigh scattering extending into the infrared. The eclipse shows a featureless blackbody-like WFC3/G141 spectrum and a weak methane absorption feature in the Spitzer 3.6 μm band. Future James Webb Space Telescope follow-up observations are needed to confirm these results.

scholarly journals Mercury vapor air–surface exchange measured by collocated micrometeorological and enclosure methods – Part II: Bias and uncertainty analysis

2015 ◽  
Vol 15 (4) ◽  
pp. 4627-4676
Author(s):  
W. Zhu ◽  
J. Sommar ◽  
C.-J. Lin ◽  
X. Feng
Keyword(s):  
Flux Measurement ◽  
Bowen Ratio ◽  
Vertical Gradient ◽  
Systematic Evaluation ◽  
Data Set ◽  
Surface Exchange ◽  
Concentration Difference ◽  
Vegetation Height ◽  
Gradient Based ◽  
Flux Quantification

Abstract. Dynamic flux chambers (DFCs) and micrometeorological (MM) methods are extensively deployed for gauging air–surface Hg0 gas exchange. However, a systematic evaluation of the precision of the contemporary Hg0 flux quantification methods is not available. In this study, the uncertainty in Hg0 flux measured by relaxed eddy accumulation (REA) method, aerodynamic gradient method (AGM), modified Bowen-ratio (MBR) method, as well as DFC of traditional (TDFC) and novel (NDFC) designs is assessed using a robust data-set from two field intercomparison campaigns. The absolute precision in Hg0 concentration difference (Δ C) measurements is estimated at 0.064 ng m−3 for the gradient-based MBR and AGM system. For the REA system, the parameter is Hg0 concentration (C) dependent at 0.069+0.022C. 57 and 62% of the individual vertical gradient measurements were found to be significantly different from zero during the campaigns, while for the REA-technique the percentage of significant observations was lower. For the chambers, non-significant fluxes are confined to a few nighttime periods with varying ambient Hg0 concentration. Relative bias for DFC-derived fluxes is estimated to be ~ ±10%, and ~ 85% of the flux bias are within ±2 ng m−2 h−1 in absolute term. The DFC flux bias follows a diurnal cycle, which is largely dictated by temperature controls on the enclosed volume. Due to contrasting prevailing micrometeorological conditions, the relative uncertainty (median) in turbulent exchange parameters differs by nearly a factor of two between the campaigns, while that in Δ C measurements is fairly stable. The estimated flux uncertainties for the triad of MM-techniques are 16–27, 12–23 and 19–31% (interquartile range) for the AGM, MBR and REA method, respectively. This study indicates that flux-gradient based techniques (MBR and AGM) are preferable to REA in quantifying Hg0 flux over ecosystems with low vegetation height. A limitation of all Hg0 flux measurement systems investigated is their incapability to obtain synchronous samples for the calculation of Δ C. This reduces the precision of flux quantification, particularly the MM-systems under non-stationarity of ambient Hg0 concentration. For future applications, it is recommended to accomplish Δ C derivation from simultaneous collected samples.

scholarly journals Large-scale assessment of antimicrobial resistance marker databases for genetic phenotype prediction: a systematic review

2020 ◽  
Vol 75 (11) ◽  
pp. 3099-3108
Author(s):  
Norhan Mahfouz ◽  
Inês Ferreira ◽  
Stephan Beisken ◽  
Arndt von Haeseler ◽  
Andreas E Posch
Keyword(s):  
Antimicrobial Resistance ◽  
Clinical Microbiology ◽  
Large Scale ◽  
Diagnostic Testing ◽  
Error Rates ◽  
Systematic Evaluation ◽  
Large Scale Assessment ◽  
Performance Requirements ◽  
Public Repositories ◽  
The Right

Abstract Background Antimicrobial resistance (AMR) is a rising health threat with 10 million annual casualties estimated by 2050. Appropriate treatment of infectious diseases with the right antibiotics reduces the spread of antibiotic resistance. Today, clinical practice relies on molecular and PCR techniques for pathogen identification and culture-based antibiotic susceptibility testing (AST). Recently, WGS has started to transform clinical microbiology, enabling prediction of resistance phenotypes from genotypes and allowing for more informed treatment decisions. WGS-based AST (WGS-AST) depends on the detection of AMR markers in sequenced isolates and therefore requires AMR reference databases. The completeness and quality of these databases are material to increase WGS-AST performance. Methods We present a systematic evaluation of the performance of publicly available AMR marker databases for resistance prediction on clinical isolates. We used the public databases CARD and ResFinder with a final dataset of 2587 isolates across five clinically relevant pathogens from PATRIC and NDARO, public repositories of antibiotic-resistant bacterial isolates. Results CARD and ResFinder WGS-AST performance had an overall balanced accuracy of 0.52 (±0.12) and 0.66 (±0.18), respectively. Major error rates were higher in CARD (42.68%) than ResFinder (25.06%). However, CARD showed almost no very major errors (1.17%) compared with ResFinder (4.42%). Conclusions We show that AMR databases need further expansion, improved marker annotations per antibiotic rather than per antibiotic class and validated multivariate marker panels to achieve clinical utility, e.g. in order to meet performance requirements such as provided by the FDA for clinical microbiology diagnostic testing.

scholarly journals Significance Testing and Multivariate Analysis of Datasets from Surface Plasmon Resonance and Surface Acoustic Wave Biosensors: Prediction and Assay Validation for Surface Binding of Large Analytes

Sensors ◽  
2018 ◽  
Vol 18 (10) ◽  
pp. 3541 ◽  
Author(s):  
Mihaela Puiu ◽  
Lucian-Gabriel Zamfir ◽  
Valentin Buiculescu ◽  
Angela Baracu ◽  
Cristina Mitrea ◽  
...  
Keyword(s):  
Surface Plasmon Resonance ◽  
Acoustic Wave ◽  
Surface Acoustic Wave ◽  
Surface Plasmon ◽  
Plasmon Resonance ◽  
Statistical Significance ◽  
Surface Binding ◽  
Experimental Conditions ◽  
Custom Made ◽  
Binding Curves

In this study, we performed uni- and multivariate data analysis on the extended binding curves of several affinity pairs: immobilized acetylcholinesterase (AChE)/bioconjugates of aflatoxin B1(AFB1) and immobilized anti-AFB1 monoclonal antibody/AFB1-protein carriers. The binding curves were recorded on three mass sensitive cells operating in batch configurations: one commercial surface plasmon resonance (SPR) sensor and two custom-made Love wave surface-acoustic wave (LW-SAW) sensors. We obtained 3D plots depicting the time-evolution of the sensor response as a function of analyte concentration using real-time SPR binding sensograms. These “calibration” surfaces exploited the transient periods of the extended kinetic curves, prior to equilibrium, creating a “fingerprint” for each analyte, in considerably shortened time frames compared to the conventional 2D calibration plots. The custom-made SAW sensors operating in different experimental conditions allowed the detection of AFB1-protein carrier in the nanomolar range. Subsequent statistical significance tests were performed on unpaired data sets to validate the custom-made LW-SAW sensors.

scholarly journals Analytical challenges of untargeted GC-MS-based metabolomics and the critical issues in selecting the data processing strategy

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 967 ◽  
Author(s):  
Ting-Li Han ◽  
Yang Yang ◽  
Hua Zhang ◽  
Kai P. Law
Keyword(s):  
Quality Control ◽  
Data Processing ◽  
Epidemiological Study ◽  
Internal Standard ◽  
Analytical Techniques ◽  
Experimental Conditions ◽  
Data Set ◽  
Raw Data ◽  
Model Based ◽  
Critical Issues

Background: A challenge of metabolomics is data processing the enormous amount of information generated by sophisticated analytical techniques. The raw data of an untargeted metabolomic experiment are composited with unwanted biological and technical variations that confound the biological variations of interest. The art of data normalisation to offset these variations and/or eliminate experimental or biological biases has made significant progress recently. However, published comparative studies are often biased or have omissions. Methods: We investigated the issues with our own data set, using five different representative methods of internal standard-based, model-based, and pooled quality control-based approaches, and examined the performance of these methods against each other in an epidemiological study of gestational diabetes using plasma. Results: Our results demonstrated that the quality control-based approaches gave the highest data precision in all methods tested, and would be the method of choice for controlled experimental conditions. But for our epidemiological study, the model-based approaches were able to classify the clinical groups more effectively than the quality control-based approaches because of their ability to minimise not only technical variations, but also biological biases from the raw data. Conclusions: We suggest that metabolomic researchers should optimise and justify the method they have chosen for their experimental condition in order to obtain an optimal biological outcome.

Closure Effects on Infrared Spectral Library Search Performance

1987 ◽  
Vol 41 (8) ◽  
pp. 1298-1302 ◽  
Author(s):  
P. B. Harrington ◽  
T. L. Isenhour
Keyword(s):  
Infrared Spectra ◽  
Analytical Method ◽  
Unit Vector ◽  
Search Performance ◽  
Spectral Library ◽  
Data Set ◽  
Library Search ◽  
Vector Length ◽  
Infrared Spectral ◽  
Noise Frequency

Closure is caused by normalization of a data set, and it affects any multivariate analytical method applied to that data set. Two common methods of normalizing infrared spectra (IR), to unit maximum absorbance and to unit vector length, are evaluated by measurement of library search performance. Search performance is evaluated, by the use of the Quantitative Reliability Metric (QRM), as a function of noise frequency and noise level.

Immediate Changes of Bone Density Caused by the Implantation of a Femoral Stem - A Dexa Study

2011 ◽  
Vol 21 (6) ◽  
pp. 706-712 ◽  
Author(s):  
Ulf G. Leichtle ◽  
Jeremi Leasure ◽  
Franz Martini ◽  
Carmen I. Leichtle
Keyword(s):  
Bone Density ◽  
Bone Loss ◽  
Femoral Stem ◽  
Periprosthetic Bone ◽  
Experimental Conditions ◽  
Press Fit ◽  
Custom Made ◽  
Femoral Stems ◽  
Cementless Prosthesis ◽  
Post Implantation

Considerable immediate periprosthetic bone density changes after implantation of femoral stems have been observed comparing DEXA measurements taken pre- and post-operatively. This is important in relation to the interpretation of DEXA studies. We analysed these density changes under standardised experimental conditions. Five human femora were implanted with a custom made femoral stem and ten femora with a standard cementless prosthesis. Densitometry was performed at various stages of implantation. Following rasping only slight density changes were noted (–2.7% to +0.7%). Comparing post-implantation and pre-operative measurements, all custom made stems with a proximal press-fit demonstrated clear increases in proximal periprosthetic bone density of +11% and +14%. In contrast, the standard prosthesis with a distal press-fit showed a loss of –5% and –2% in the proximal zones. Measurements following removal of the implants demonstrated hardly any density changes (0% to –4%) compared to the pre-operative measurements. We concluded that compacting of trabecular bone or bone loss due to rasping are not the main causes of density changes. Substantial measuring errors exist. For examination of periprosthetic bone density changes, pre-operative initial measurements should not be used as a baseline for comparison. Studies should commence with an immediate postoperative measurement.

Automatic categorization of Web service elements

2018 ◽  
Vol 14 (2) ◽  
pp. 233-258 ◽  
Author(s):  
Efthimia Mavridou ◽  
Konstantinos M. Giannoutakis ◽  
Dionysios Kehagias ◽  
Dimitrios Tzovaras ◽  
George Hassapis
Keyword(s):  
Web Services ◽  
Web Service ◽  
Semantic Annotation ◽  
Third Party ◽  
Systematic Evaluation ◽  
Evaluation Procedure ◽  
Data Set ◽  
Content Type ◽  
Semantic Categorization ◽  
Description File

Purpose Semantic categorization of Web services comprises a fundamental requirement for enabling more efficient and accurate search and discovery of services in the semantic Web era. However, to efficiently deal with the growing presence of Web services, more automated mechanisms are required. This paper aims to introduce an automatic Web service categorization mechanism, by exploiting various techniques that aim to increase the overall prediction accuracy. Design/methodology/approach The paper proposes the use of Error Correcting Output Codes on top of a Logistic Model Trees-based classifier, in conjunction with a data pre-processing technique that reduces the original feature-space dimension without affecting data integrity. The proposed technique is generalized so as to adhere to all Web services with a description file. A semantic matchmaking scheme is also proposed for enabling the semantic annotation of the input and output parameters of each operation. Findings The proposed Web service categorization framework was tested with the OWLS-TC v4.0, as well as a synthetic data set with a systematic evaluation procedure that enables comparison with well-known approaches. After conducting exhaustive evaluation experiments, categorization efficiency in terms of accuracy, precision, recall and F-measure was measured. The presented Web service categorization framework outperformed the other benchmark techniques, which comprise different variations of it and also third-party implementations. Originality/value The proposed three-level categorization approach is a significant contribution to the Web service community, as it allows the automatic semantic categorization of all functional elements of Web services that are equipped with a service description file.

On magdalenian mobility and land use in north-west Europe

1995 ◽  
Vol 2 (2) ◽  
pp. 85-104 ◽  
Author(s):  
Eelco Rensink
Keyword(s):  
Systematic Evaluation ◽  
Upper Palaeolithic ◽  
Hunter Gatherers ◽  
Data Set ◽  
North West ◽  
Archaeological Data ◽  
Relative Dating ◽  
New Directions ◽  
History Of ◽  
History Of Europe

Investigations into the upper palaeolithic settlement history of Europe have made significant advances over the past decades in several fields. As a result of the reappraisal of old collections and the excavation of ‘new’ sites, an extensive data set has become available which can be used to study aspects of the organization of palaeolithic hunter-gatherers. The improvement of absolute and relative dating methods has provided the archaeologist with a more solid chronological framework. Additionally, innovations in archaeological theory and methodology have led to the exploration of new directions of inquiry. This paper focuses on a well-known example of these new directions: the study ofregionalsettlement-subsistence systems of palaeolithic groups, incorporating the systematic evaluation of archaeological data recovered from substantial areas. A growing number of archaeologists dealing with the upper palaeolithic record and active in various regions throughout Europe is currently engaged in this particular form of analysis (Audouze 1992; Hahn 1987; Julien 1987; Straus 1986; Weniger 1987, 1989).

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